The Shadow Journeys Original Journey Indigo League Part 1 of 4
by Dark-Arceus
Summary: 25 years ago Shade INC appeared from nowhere and set up shop everywhere. They were led by a mystery Mr Shade. Now Shadow Pokemon have appeared all over the land and The evil Team Shadow has taken over. This is the story of Ash and how with the help of his Pikachu, his friend Yellow and The mysterious Grey fight against the Shadow Pokémon threat.
1. Prologue

**The Shadow Journeys: Original Journey: Indigo League Part 1**

**Kind of Follows the Pokémon Anime Episodes but with the Shadow Pokémon twist**

**Each normal chapter is based around an Episode**

**Prologue**

_25 years ago Shade INC appeared from nowhere and set up shop everywhere. They were led by a mystery Mr Shade and he brought out Silph Co, The Battle Frontiers, The Pokéathlon Domes, Safari Zones, The Devon Corporation, The Pokémon Contests, The Pokétch Company, Many Mines, Cycle Shops, Gyms, The Leagues and much, much more. Five years after Shade INC was built a mystery black helicopter was somewhere between Orre and Johto was heading towards Mount Silver, on board were a_ _Dark Ball taken from a member of Team Rocket called Iron-Masked Marauder, a Large machine stolen from Cipher and The Shadow Crystal taken from Chroma Ruins in the Almia Region. The mystery helicopter had a white S on the side. Piloting the helicopter was a Meowth known to Team Shadow as Nocturnal. He said into a microphone to Mr Shade in perfect English "I got the machine from Cipher boss"_

_Mr Shade said "Well Done Nocturnal, Soon my master plan will come into effect and we will take over fully and create a army of shadow slaves"_ _The mystery helicopter then vanished into the clouds towards a massive tower on top of Mount Silver._

_A middle aged man known as Grey was sitting in the middle of the forest with his eyes closed and he sensed that the helicopter reached Mount Silver and he nodded and thought to himself now it's time to find the chosen one. _

_The years went by until the time reached for a special trainer to start his journey, the trainer with the power to defeat the shadow Pokémon and the masters behind them. This is the story of Ash and how with the help of his Pikachu, his new friend Yellow and The mysterious Grey fight against the Shadow Pokémon threat._


	2. Pikachu, I Choose You

**The Shadow Journeys: Original Journey: Indigo League Part 1**

**Kind of Follows the Pokémon Anime Episodes but with the Shadow Pokémon twist**

**Each normal chapter is based around an Episode**

**Chapter One Pikachu, I Choose You**

A Nidorino and a Gengar are exchanging attacks in a battle. After Nidorino dodges Gengar's attack, it leaps at it. The scene seamlessly comes to life as the small game screen enlarges and the monochrome Pokémon gain color and two are battling in a stadium at the Pokémon League, watched by crowds of fans. Gengar dodges Nidorino's Horn Attack, and then jumps on its head. It leaps backward and successfully puts its opponent to sleep with Hypnosis. As Nidorino falls asleep, its Trainer returns it to its Poké Ball and then throws out another to take its place. Gengar jumps back as an Onix comes out. It tries to Tackle into Gengar head-first, but misses and hits the battlefield instead. It pulls back up, unfazed. This battle is being watched on television by a boy from Pallet Town named Ash Ketchum. He is now ten years old, which means he can become a Pokémon Trainer soon. The Battle then gets interrupted by the news. The news was hosted by a red haired woman. She said "This just in the Head of Rocket Industry and the Gym Leader of Viridian Gym, the Chief Executive Giovanni John Sakaki was attacked yesterday by Shadow Nidorans as he was heading towards the Rocket owned Lab run by Professor Oak and our experts say that Shadow Pokémon are on the rise near Viridian City. Executive Petrel Lambda will take Giovanni place at handing out the new Pokémon to new trainers and Director James Kojiro said that the Shadow Pokémon are being researched to find a way to purify them. In other news the police are still puzzled of how the whole Orre region was destroyed nine years ago by Team Shadow" Tomorrow, Ash will receive a starter Pokémon from Professor Oak and his friend Grey. Ash was a raven haired boy with brown eyes. He was wearing a special hat which looked like half a poke ball. It was a gift from Grey. He is going to start his Pokémon journey with Yellow, on the long quest of his dream of becoming a Pokémon Master and to help find a way to stop the Shadow Pokémon.

His mother Delia enters the room and reminds him "Ash it is 11 o'clock at night and you should be asleep" Delia was a 29 year old woman who had amber brown eyes and mahogany brown hair.

Ash complains to his mother "I'm too excited to fall asleep"

As a compromise, his mother changes his television's channel to Professor Oak's lecture on Shadow Pokémon and tells him "Fine you can go to bed when the program is finished and make sure you go to Oaks lab in the morning when you wake up as Grey wants to see you as he has a gift for you". That night, he dreams about deciding which starter Pokémon he wants not knowing that Grey will give him something different. First, he dreams of choosing and sending out Bulbasaur then Squirtle and finilly dreams of choosing Charmander. The night turns to morning, and Ash, still in bed, dreams of fighting off lots of Shadow Pokémon with all three starters. Suddenly, he suddenly awakens to find that he has thrown his Voltorb-shaped alarm clock in his sleep, breaking it against a wall as a result. Afraid that he might have overslept and missed Grey as Grey was a busy man, Ash runs out of his house in his pyjamas and shoes to get to Professor Oak's Laboratory. Pallet Town was a small town with dirt trails and wide open grass fields. Professor Oak's Laboratory stands out in Pallet Town for its wind turbine, the three windows of the inner balcony, and for the four windows of the second floor. The lab is composed of two floors. Inside the entrance door is a hallway with several doors, and to the left is a chest of drawers and the stairway to the second floor. The Oak Corral is a natural environment for Pokémon development. It is divided into regions according to type; there are areas that are perfect for Rock Pokémon, desert areas for Ground and Fire types, grassy regions, and several lakes. Pallet Town has a very small an airport just to the west and that and the rest of the town was surrounded by a large wall with towers to keep out any Shadow Pokémon. This was run by Rocket Industry to also keep out Shade INC. Outside the laboratory, a crowd of people have gathered, including a group of cheerleaders. Ash pushes through and bumps into his rival, the professor's grandson, Gary Oak. Gary Oak was also ten but he had brown hair and black eyes. He was wearing blue top and black trousers.

Gary taunts "Hello Ashy-boy you late which doesn't look good". He then tells Ash "I am already received my starter Pokémon from my grandfather and Executive Petrel" He then boasts to the crowd "I will make Pallet Town famous by becoming a Pokémon Master"

Ash, however, is more interested in asking "Hey Gary which starter did you chose?"

Gary only tells him "It was the best one"

Before Ash can fully express his frustration, a voice said "Mr Oak I don't think you have the best one as they are only as great as the trainer"

Gary froze at the voice and Ash said "Hello Grey" Grey had short white hair and black eyes. He was wearing a black suit. Gary then quickly leaves in a red sports car, followed by the crowd.

Grey says with a smile "it's good to see you Ash" Grey and Ash entered the lab and Professor Oak and Executive Petrel approached them. Professor Samuel Oak was a man with grey hair and black eyes. He was wearing a lab coat over his clothes. Petrel was a younger man with purple hair and black eyes. He was wearing a black suit with white gloves, belt and boots with a little red R on it on his front pocket.

Ash's mood changes from anger to excitement as he asks "Can I get a Pokémon now Professor" before asking Grey "Where's Yellow?"

Grey said "She is waiting just outside town as she was looking into something" Professor Oak and Petrel seem doubtful that he is ready since he has shown up in his pyjamas, but Grey says "I insist that he is" Grey then pulled Petrel aside to have a quiet word. Three Poké Balls are set up on a storage device. Ash decides that he would like to start with Squirtle, but when he opens the Poké Ball, he finds that it is empty.

Professor Oak tells him "This Pokémon was taken by a Trainer who was not late". After this, Ash decides he would like Bulbasaur, but this Poké Ball is also empty. He has no choice but to go for the last choice, Charmander, but the final Poké Ball is also empty. The three were all taken by Trainers who arrived on time, and it seems that there is no Pokémon left for Ash. Professor Oak reluctantly tells him "I sorry Ash"

Grey then says "Not to worry as I already got one for you and it will help defeat any Shadow Pokémon you should come across" He pulls out a Poké Ball appears that has a lightning bolt mark on it. Grey hands the Poké Ball to Ash. With a flash of light, Pikachu comes out of the Ball. Ash loves the cute Pokémon, picks it up, and hugs it. Pikachu get too excited and shocks Ash with an electric attack.

Petrel hands Ash a Pokédex and six Poké Balls (all with small red Rs) but gets shocked as well when he touches Ash, He they says "These are specially built models that are not traceable by Shade INC and if you need more Poke balls contract Rocket Industry" When Ash steps outside the laboratory, he finds a small crowd has gathered to cheer him on as well, including his mother, who is sad to see him leaving.

She gives him his backpack full of supplies and starts explaining "I packed everything you should need". Ash gets embarrassed when she reminds him "Remember to change your underwear every day"

Ash pulls his bag away from her, telling her "Mom you are embarrassing me"

She sees Pikachu and said "I wonder why it is not in its Poké Ball" Ash tries to get it in, but it hits the Ball back every time.

Delia says "It is cute that you and Pikachu are playing catch, you must be great friends already"

Ash replies with a smile "Yeah we are great buddies who will help me become a Pokemon Master" Pikachu shocks the entire crowd with its electricity in excitement. Ash waves bye and he with Pikachu on his shoulder. Ash leaves the safety of the town and into the forest. After getting tired of walking, he tries to talk to Pikachu only to find out that Pikachu cannot say anything but its name. He then realized he was an idiot as Yellow already taught him that. He tries to convince it to get back in its Poké Ball, and pulls out his new Pokédex for information on it. His Pokédex explains that Pokémon must be kept in the Poké Ball. Then Pikachu clicks it and it explains that not all Pokémon like to be kept in Poké Balls. He then thanks Pikachu who looked like he was grinning. A Pidgey walks out near them and Ash scans it with his Pokédex for more information. The Pokédex tells him everything including that it wasn't a Shadow Pokémon which shocked Ash but he then thought that Grey added it on to it. He is eager to catch it, Pikachu looks excited and faced off against it. Ash decides to catch the Pidgey without Pikachu's help. He throws a Poké Ball at it, but the Pidgey breaks out easily. The Pokédex explains that a Pokémon should be weakened before it can be caught. Pikachu laughs at Ash. Ash then was glad that Yellow wasn't there as she would laugh then start telling him off. Frustrated, Ash tries again, this time sending Pikachu to fight Pidgey, but the bird blows him off with a Gust and then hits him with a Sand-Attack, before flying away. Ash turns and sees that a Rattata is digging through his bag. He scans it with his Pokédex, which mentions that Rattata is a forest Pokémon. Just as Ash was questioning why it came out into the field in his head, the Pokédex explains that it sometimes leaves its habitat to steal from stupid travellers. Pikachu laughs at Ash who then glared at Pikachu who stopped laughing. Ash turns and notices a group of Pidgey in the field. He throws a rock at them in anger, which only scares them away. However, he sees another bird Pokémon with black eyes in the field and throws a rock at it, which hits it in the back of its head. When it turns to look at him, however, he realizes that he did not hit a Pidgey; he scans it with his Pokédex and learns that it is a Spearow which is considerably less docile than a Pidgey and this one is a Shadow Pokémon. Ash gulps as the Shadow Spearow swoops down at him several times to attack him. The Shadow Spearow then spots and targets Pikachu instead. The Pokédex explains Shadow Pokémon are more aggressive than normal Pokémon. Just as the Shadow Spearow is about to hit Pikachu, Pikachu shocks it with an Electric attack, and it is knocked out of the sky. Ash and Pikachu relax however the Shadow Spearow cries for help. Ash and Pikachu start running away from a flock of Shadow Spearow who appear from nowhere. Pikachu runs ahead of Ash and the Shadow Spearow fly after it, attacking it until it falls to the ground. The Shadow Spearow start swarming around it, but Ash grabs the injured Pikachu and runs straight to a waterfall. He jumps into the river below to escape The Shadow Spearow and is dragged into a large pond, narrowly swimming out of the path of a Gyarados. On the shore of this pond, a girl is fishing waiting for any Shadow Pokémon to appear. She pulls out Ash and Pikachu. Ash asked "Yellow is that you?" The girl was 10 and she had blond hair and brown eyes. She had a straw hat which hides a ponytail. She was wearing brown explorer gear. She also had a slate-gray fox-like Pokémon with red and black accents on its head and feet with triangular ears known as Zorua which Ash was told form a far way region.

She said "Yes it me Ash" She then tells him "We need go to the Pokémon Center in Viridian City so Pikachu can heal" She then starts walking off and at that moment, Ash hears the distant cries of The Shadow Spearow. He turns to see the flock flying toward him from afar. They quickly start running towards Viridian City after Yellow grabbed Zorua, with storm clouds forming above them and the flock of Shadow Spearow in close pursuit. Soon, it starts to rain. So Ash and Yellow grab an orange haired girl's bike before she said anything. Ash and Yellow ride until the bike trip over a ledge and they fall to the ground. Ash finds himself looking at his injured Pikachu lying on the ground, with the Shadow Spearow approaching and the storm growing worse.

Desperate to save his Pokémon, he leaves Pikachu's Poké Ball next to it and tells him "Get inside for safety" Ash then spreads out his arms and stands before the Shadow Spearow, telling them "Attack Me"

Yellow stands knowing something Ash didn't and she said "Yes Attack us" However, just as The Shadow Spearow are diving upon Ash, Pikachu leaps up and over Ash's shoulder while Zourua looking like a Pikachu jumped over Yellow's shoulder to confront the flock of Shadow Spearow. The lightning from the storm is drawn to Pikachu, striking it and vastly increasing its power. Pikachu helped by Zorua unleashed a massive discharge of electricity that lights up the dark sky and takes out the entire flock of Shadow Spearow, as well as the orange haired girl's bike. The Shadow Spearow were turned back into normal Spearow. Unknowing to them one of The Shadow Spearow escaped and flew west. Pikachu and Zorua are drained of stamina from the effort. Once the storm has cleared Ash, Yellow, Zorua and Pikachu both rise from the ground, exhausted but victorious. Ash and Yellow looked up and sees a shimmering, golden Pokémon majestically flying through the sky and over the rainbow that had been left after the storm and Ash's Pokédex is unable to identify the species. Ash and Yellow continue on to Viridian City with Ash carrying Pikachu and Yellow carrying Zorua. Ash receives a lick from Pikachu and Ash smiled at Yellow at their victory. They then trek toward Viridian, still in need of the Pokémon Center, but they briefly take the time to wonder what else lies ahead of them on their journey.

_Next_ _Shadow Pokémon Emergency_


	3. Shadow Pokemon Emergency

**The Shadow Journeys: Original Journey: Indigo League Part 1**

**Kind of Follows the Pokémon Anime Episodes but with the Shadow Pokémon twist**

**Each normal chapter is based around an Episode**

**Chapter Two Shadow Pokémon Emergency**

After the battle with the Shadow Spearow, Pikachu is badly injured and Zorua was tired. Ash and Yellow are on the way to the Viridian City Pokémon Centre as Ash took what Yellow said earlier so he can take Pikachu there to be healed. Viridian City is a small city located in western Kanto. Three major paths lead from the city centre. To the north is Route 2, as well as Viridian Forest, which lies in the middle of the route, leading to Pewter City. To the south is Route 1, which leads to Pallet Town. To the west is Route 22, leading to Indigo Plateau and the Pokémon League. Giovanni serves as Gym Leader of the Ground-specialist Viridian Gym, but the Gym is locked as Giovanni is still at the hospital. As they enter the town, Ash and Yellow are stopped by an Officer Jenny who works indirectly for Mr Shade and Shade INC. Jenny is the shared last name of Jenny family, in which most members are police officers and maintain the law and order. Officer Jennies are often accompanied by Growlithe or a particular Pokémon that is of importance in a town or a personal preference to that Jenny like Wobbuffet, Spinarak or even a Chatot. The only differences are the symbols on their hats and their uniforms. They also had a black s in the middle of the symbol. Officer Jenny finds it suspicious that he is carrying Pikachu in his arms and not in a Poké Ball. She also finds it suspicious that Yellow was carrying Zorua. She said "Excuse me Sir and Madam I need you to show ID as there have been thieves and Team Shadow in the area" Ash is unsure how to prove his identity, but Yellow pulls out the Pokédexes which she know acts as IDs.

Yellow said "Here you go Officer" Officer Jenny looks and them and gasps after seeing Yellows Name.

Officer Jenny asked "Yellow as in one of the Grey's trainees?"

Yellow said "Yes"

Officer Jenny asked "give my regards to Grey when you see him, I see you again Yellow and Red" Officer Jenny drives on away on a motorbike.

Ash asked Yellow "Red?"

Yellow Said "All of Grey trainees are named like I'm called Yellow but as you know that not my true name but it's the name I like so if you want you could be Red or Ash or even both anyway we need to go as I need to talk with Grey" Ash, Yellow, Pikachu and Zorua headed towards the Pokémon Centre leaving behind the orange haired girl who had just arrived carrying the scorched remains of her bicycle. Angrily, she runs after them. On a nearby wall was a wanted poster showing the pictures the most wanted criminal who was Nocturnal who was wanted for various crimes. A grappling hook reaches down and pulls the poster up into the same mystery helicopter that had a white S which is hovering overhead. There were two Grunts looking at the picture Nocturnal. The Shadow Grunts looked like the old Team Rocket Grunts but with a white S. One Grunt said "We got the picture sir"

Nocturnal said "Good as Mr Shade wants us to attack the Pokémon centre as he heard that one or two of Grey's trainees are there and Mr Shade wants them gone"

Meanwhile Ash, Yellow, Pikachu and Zorua arrive at the Pokémon Centre. Yellow vanished as soon as she entered leaving Ash with the two Pokémon. Ash went over to Nurse Joy. Nurse Joy are a family of kind nurses who take care of Pokémon. Joy is not the first name of these women, but actually the family name. They also work indirectly for Mr Shade. This Pokémon Centre's Nurse Joy takes Pikachu away on a stretcher; She scolds "Young man you shouldn't allow the Pikachu to have become so badly hurt or the other Pokémon to become exhausted "

Ash feels crestfallen and decides to call home so he asks "How do I call home"

Nurse Joy softens and said "over there dear" while pointing to some video screens. He presses a button and His mother appeared.

Delia said "Hey Ash what's the matter"

"Pikachu was hurt by some Shadow Spearow on the way here" said Ash

Delia said "Grey said to me just before he left that the only failure is when you can't see your failures and he also told me that Pokémon from the best trainers get hurt"

Ash said "Thank you Mom" Delia signed off and Ash is then called by Professor Oak.

Professor Oak looked surprised and it shown when he said "You reached Viridian so soon" Ash tells him about the unidentified bird Pokémon he saw fly over the rainbow.

Oak does not believe him saying "Many Trainers have never seen that Pokémon even after searching their entire lives. I wish good luck" He was about to hang up when Executive Petrel appeared next to Oak.

Executive Petrel said "I see that you already met up with shadow Pokémon which is worrying new to me so I wanted to inform you that I have something for you so be on the lookout for my courier known as Domino Green or just Green as she likes to be known as" He hangs up as Yellow reappears.

Yellow said to Ash "I just got into contract with Grey and sorry for letting you have a chance to talk to him. Anyway Grey wasn't happy about the Shadow Spearow so he is going to meet us at Pewter City" At that moment, Misty enters the Pokémon Centre with her destroyed bike.

She stormed over to Ash and said angrily "Your Pikachu destroyed my bike"

Ash tries to explain "Pikachu was injured badly by some shadow Pokémon" but Misty wouldn't listen. Yellow pulled the girl to one side and whispered something which not noticed by Ash and Misty paled.

Misty quickly inquires "How is Pikachu's recovery?"

Ash said "I don't know and not be rude I'm Ash and this is Yellow"

Misty said "I'm Misty" just as Nurse Joy brings Pikachu and Zorua in. An alarm goes off, warning of the approach of Team Shadow's helicopter. Team Shadow launches an attack on the Pokémon Centre and their Poké Balls smash through the glass roof releasing an Ekans and a Koffing. Koffing floods the room with smoke, under the cover of which the two grunts known as Dusk and Twilight enter with Nocturnal. Dusk was a male grunt and Twilight was a female grunt. Nurse Joy begins transferring Pokémon to the safety of the Pewter City Pokémon Centre to protect them from Team Shadow's clutches and to prevent them from turning into Shadow Pokémon.

Nocturnal said "Hand all the Pokémon over or I will be force to use force"

Yellow said No" and She, Ash and Misty attempt to fight off Team Shadow. At Yellows urging, Ash releases a Pidgey and a Rattata from Poké Balls that have been knocked to the floor, but they are easily defeated by Twilight's Ekans. Misty sends out a Goldeen, but it flops around uselessly due to the lack of water which causes Yellow to grin as she releases a Vulpix. Vulpix went up against Nocturnal who was an even match. Ash seeing that he has nothing to do flees, pushing Pikachu and Zoura's stretcher, but the stretcher runs into a thick cord and overturns. Pikachu and Zoura are catapulted into the air and lands among a group of Pikachu that power the Centre's backup generator and powered by Ash riding quickly on Misty's burnt bicycle, Pikachu and Zoura hits Dusk and Twilight with a powerful ThunderShock attack. As they take the electricity, Koffing expels a large amount of poisonous gas in pain. The gas reacts to the electricity, and the result is a colossal explosion that destroys much of the Pokémon Centre causing everyone to flee the centre. Officer Jenny arrives too late to do anything except watch the explosion.

Meanwhile the Shadow Trio managed to retreat to the helicopter. Nocturnal said to the other two "I think we met with Red the newest member of Grey team so Red is what Grey was planning, Dusk I think we need to see Mr Shade" The Helicopter quickly left using the smoke as cover.

As this was all happing, Grey was in Viridian Forest with a Mr Ice who is the leader of the Sinis Trio, the head of the branch of Team Shadow that was known as Team Dim Sun but was now called Shadow Sun which was now researchers working for Mr Shade. Mr Ice wore blue and had blue hair. He said as grey reached him "we meet again Grey but as you can guess I won't be around for long, Froslass time to disappear" He disappeared with a smirk on his face in front of Grey who was irritated that Mr Ice managed to outthink him again. He was hunting Mr Ice as it was Mr Ice who helped Mr Shade with creating the Shadow Pokémon.

The next day, Ash, Yellow, Pikachu and Zorua left Viridian City and headed for Viridian Forest with Misty in tow much to Yellow annoyance as she didn't like her much. Then Ash spotting a wild Caterpie and threw a Poké Ball in the hope of capturing it.

_Next_ _Ash Catches a Caterpie_


End file.
